Hunor, you could post a pic of the geometry.
Patterning 1000 cubes on a flat surface is one thing, but the geometry is curved, that's another.
Solidworks has one option really "Geometry Pattern". If it is checked, then end conditions of the patterned feature are not solved for each pattern instance and each instance is identical geometry to the parent or seed feature. Unchecked (the default) means it does solve end condition. So if the end condition was "up to surface", then each instance will solve for that surface meaning the extrude depth varies for each which of course takes longer.
The other option "Verification on Rebuild" in Tools/Options/Performance if checked applies additional error checking and can slow down rebuilds. It affects everything in the tree. Depending on the complexity of the geometry, rebuilds can be quite a bit slower with this option on. The irony here is, the more complex geometry which is already slow to rebuild really needs this option on to be sure the model is "tight".
Anyway, so I would try these otions and see if that helps. And may show us a pic and explain how you are going about creating this.
Jason
UG NX2.02.2 on Win2000 SP3
SolidWorks 2005 SP5.0 on WinXP SP2
SolidWorks 2006 SP3.0 on WinXP SP2